Using network theory on an integrated time-resolved genome-wide gene expression data, we investigated intricate dynamic regulatory relationships of transcription factors and target genes to unravel signatures that contribute to extreme phenotypic differences in yeast, Saccharomyces cerevisiae. We performed comparative analysis of gene expression profiles of two yeast strains SK1 and S288c, which lie at extreme ends of sporulation efficiency. The results based on various structural attributes of the networks, such as clustering coefficient, degree-degree correlations and betweenness centrality suggested that a delay in crosstalk between functional modules can be construed as one of the prime reasons behind low sporulation efficiency of S288c strain. A more hierarchical structure in late phase of sporulation in S288c seemed to be an outcome of a delayed response, resulting in initiation of modularity, which is a feature of early sporulation phase. Further, weak ties analysis revealed meiosis-associated genes for the high sporulating SK1 strain, while for the low sporulating S288c strain it revealed mitotic genes. This was a further indication of delay in regulatory activities essential to initiate sporulation in S288c strain. Our results demonstrate the potential of this framework in identifying candidate nodes contributing to phenotypic diversity in natural populations.